seqfish-v0.0.yaml

files:
  -
    example: 'codebook/channel_1.tsv'
    pattern: 'codebook/channel_[0-9]+\.(tsv|csv)'
    description: 'Barcodes.'
    required: True
    is_qa_qc: False    
  -
    example: 'HybCycle_10/MMStack_Pos12.ome.tif'
    pattern: 'HybCycle_\d+/MMStack_Pos\d+\.ome\.tiff?'
    description: 'Raw OME-TIFF images with a variable number of field of views, and slices per tissue.'
    required: True
    is_qa_qc: True
  -
    example: 'initial_background/MMStack_Pos11.ome.tif'
    pattern: 'initial_background/MMStack_Pos\d+\.ome\.tiff?'
    description: 'Raw OME-TIFF image of image without probes before imaging hybridizations; used for background and autofluorescence removal.'
    required: True
    is_qa_qc: True
  -
    example: 'final_background/MMStack_Pos11.ome.tif'
    pattern: 'final_background/MMStack_Pos\d+\.ome\.tiff?'
    description: 'Raw OME-TIFF image of image without probes after all other hybridizations; used for background and autofluorescence removal.'
    required: True
    is_qa_qc: True
  -
    example: 'segmentation/MMStack_Pos3.ome.tif'
    pattern: 'segmentation/MMStack_Pos\d+\.ome\.tiff?'
    description: 'Labels TIFF image for segmentation.'
    required: True
    is_qa_qc: False
  -
    example: 'segmentation/raw_images/dapi_Pos19.tif'
    pattern: 'segmentation/raw_images/dapi_Pos\d+\.tif'
    description: 'DAPI TIFF image.'
    required: True
    is_qa_qc: False
  -
    example: 'segmentation/raw_images/membrane_Pos52.tif'
    pattern: 'segmentation/raw_images/membrane_Pos\d+\.tif'
    description: 'Membrane TIFF image.'
    required: False
    is_qa_qc: False
  -
    pattern: 'omexml/.*'
    description: 'Folder containing metadata for each image.'
    required: False
    is_qa_qc: False
  -
    example: 'positions.pos'
    pattern: 'positions\.pos'
    description: 'Micro-Manager coordinates of each field of view tile.'
    required: True
    is_qa_qc: False
  -
    example: 'fovinfo.csv'
    pattern: 'fovinfo\.csv'
    description: 'Upperleft coordinates for each field of view in the file extras/SlideExplorer.tif.'
    required: True
    is_qa_qc: False
  -
    example: 'extras/SlideExplorer.tif'
    pattern: 'extras/SlideExplorer\.tif'
    description: 'Overview TIFF image for all fields of view.'
    required: False
    is_qa_qc: False
  -
    pattern: 'codebook.csv'
    description: 'CSV containing codebook information for the experiment. Rows are barcodes and columns are imaging rounds. The first column is the barcode target, and the following column IDs are expected to be sequential, and round identifiers are expected to be integers (not roman numerals).'
    required: True
    is_qa_qc: False
  -
    pattern: 'metadata.json'
    description: 'Contains parameters needed to run spatial-transcriptomics-pipeline, including a description of the input data layout, image processing steps, and the decoding method to be used.'
    required: True
    is_qa_qc: False
  -
    pattern: extras\/.*
    required: False
    description: Folder for general lab-specific files related to the dataset. [Exists in all assays]